Connectivity and vagility determine spatial richness gradients and diversification of freshwater fish in North America and Europe

The latitudinal species richness gradient (LRG) has been the subject of intense interest and many hypotheses but much less consideration has been given to longitudinal richness differences. The effect of postglacial dispersal, determined by connectivity and vagility, on richness was evaluated for the species‐poor European and North American Pacific and species‐rich Atlantic regional freshwater fish faunas. The numbers of species, by habitat, migration and distributional range categories, were determined from regional species lists for these three realms. The current orientation and past connections of drainage channels indicate that connectivity is greatest in the Atlantic and least in the Pacific. With increasing connectivity across realms, endemism decreased and postglacial recolonization increased, as did the LRG slope, with the greatest richness difference occurring between southern Atlantic and Pacific regions. Recolonizing species tended to be migratory, habitat generalists and from families of marine origin. Diversification, as indicated by species/genus ratios, probability of diversification, taxonomic distinctness and endemicity, declined with increasing latitude in all realms and was least in Europe. Richness patterns are consistent with an LRG driven by the time available for postglacial recolonization and by differences in dispersal ability, with richness differences across realms reflecting differences in dispersal and diversification.     

Speciation reversal and biodiversity dynamics with hybridization in changing environments

A considerable fraction of the world's biodiversity is of recent evolutionary origin and has evolved as a by-product of, and is maintained by, divergent adaptation in heterogeneous environments. Conservationists have paid attention to genetic homogenization caused by human-induced translocations (e.g. biological invasions and stocking), and to the importance of environmental heterogeneity for the ecological coexistence of species. However, far less attention has been paid to the consequences of loss of environmental heterogeneity to the genetic coexistence of sympatric species. Our review of empirical observations and our theoretical considerations on the causes and consequences of interspecific hybridization suggest that a loss of environmental heterogeneity causes a loss of biodiversity through increased genetic admixture, effectively reversing speciation. Loss of heterogeneity relaxes divergent selection and removes ecological barriers to gene flow between divergently adapted species, promoting interspecific introgressive hybridization. Since heterogeneity of natural environments is rapidly deteriorating in most biomes, the evolutionary ecology of speciation reversal ought to be fully integrated into conservation biology.     

Phosphorus accumulates faster than nitrogen globally in freshwater ecosystems under anthropogenic impacts

Combined effects of cumulative nutrient inputs and biogeochemical processes that occur in freshwater under anthropogenic eutrophication could lead to myriad shifts in nitrogen (N):phosphorus (P) stoichiometry in global freshwater ecosystems, but this is not yet well‐assessed. Here we evaluated the characteristics of N and P stoichiometries in bodies of freshwater and their herbaceous macrophytes across human‐impact levels, regions and periods. Freshwater and its macrophytes had higher N and P concentrations and lower N : P ratios in heavily than lightly human‐impacted environments, further evidenced by spatiotemporal comparisons across eutrophication gradients. N and P concentrations in freshwater ecosystems were positively correlated and N : P was negatively correlated with population density in China. These results indicate a faster accumulation of P than N in human‐impacted freshwater ecosystems, which could have large effects on the trophic webs and biogeochemical cycles of estuaries and coastal areas by freshwater loadings, and reinforce the importance of rehabilitating these ecosystems.     

Changes in the composition of British butterfly assemblages over two decades

Changes in the abundance and distribution of individual species have been widely documented in Britain and other countries in recent decades, but little has been done to determine changes in community composition over broad geographic areas. Here, we studied species turnover in 51 butterfly assemblages in Britain since 1976, examining extinction and colonisation events together with variation in the abundances of the species. We showed that the species turnover that occurred over 20 years in Britain was associated with colonisation and extinction events and also with variability in the abundance of the species. These changes in community composition differed according to the habitat requirements of the species and their previous distributions, being more evident for habitat specialists and for southerly distributed species. Colonising species often became abundant components of the communities they joined, although this was more evident for generalist than for specialist species. The abundance of species following their arrival, increased with time since colonisation. Species turnover associated with southerly species expanding northwards is consistent with being a response to climate change. The results suggest that climate- and habitat-driven changes in the identity and abundance of species within communities are widespread, and probably ubiquitous. Similar changes are likely to be occurring in other groups of organisms that are similarly undertaking major range shifts associated with climate change.     

Geographic patterns and environmental correlates of taxonomic and phylogenetic beta diversity for large-scale angiosperm assemblages in China

A full understanding of the origin and maintenance of β-diversity patterns in a region requires exploring the relationships of both taxonomic and phylogenetic β-diversity (TBD and PBD, respectively), and their respective turnover and nestedness components, with geographic and environmental distances. Here, we simultaneously investigated all these aspects of β-diversity for angiosperms in China. Specifically, we evaluated the relative importance of environmental filtering vs dispersal limitation processes in shaping β-diversity patterns. We found that TBD and PBD as quantified using a moving window approach decreased towards higher latitudes across the whole of China, and their turnover components were correlated with latitude more strongly than their nestedness components. When quantifying β-diversity as pairwise distances, geographic and climatic distances across China together explained 60 and 53% of the variation in TBD and PBD, respectively. After the variation in β-diversity explained by climatic distance was accounted for, geographic distance independently explained about 23 and 12% of the variation in TBD and PBD, respectively, across China. Overall, our results suggest that environmental filtering based on climatic tolerance conserved across lineages is the main force shaping β-diversity patterns for angiosperms in China.     

The meaning of birth and death (in macroevolutionary birth-death models)

Birth–death models are central to much macroevolutionary theory. The fundamental parameters of these models concern durations. Different species concepts realize different species durations because they represent different ideas of what birth (speciation) and death (extinction) mean. Here, we use Cenozoic macroperforate planktonic foraminifera as a case study to ask: what are the dynamical consequences of changing the definition of birth and death? We show strong evidence for biotic constraints on diversification using evolutionary species, but less with morphospecies. Discussing reasons for this discrepancy, we emphasize that clarity of species concept leads to clarity of meaning when interpreting macroevolutionary birth–death models.     

Geographic range size, life history and rates of diversification in Australian mammals

Abstract What causes species richness to vary among different groups of organisms? Two hypotheses are that large geographical ranges and fast life history either reduce extinction rates or raise speciation rates, elevating a clade's rate of diversification. Here we present a comparative analysis of these hypotheses using data on the phylogenetic relationships, geographical ranges and life history of the terrestrial mammal fauna of Australia. By comparing species richness patterns to null models, we show that species are distributed nonrandomly among genera. Using sister‐clade comparisons to control for clade age, we then find that faster diversification is significantly associated with larger geographical ranges and larger litters, but there is no evidence for an effect of body size or age at first breeding on diversification rates. We believe the most likely explanation for these patterns is that larger litters and geographical ranges increase diversification rates because they buffer species from extinction. We also discuss the possibility that positive effects of litter size and range size on diversification rates result from elevated speciation rates.     

Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions

Diversification rate is one of the most important metrics in macroecological and macroevolutionary studies. Here I demonstrate that diversification analyses can be misleading when researchers assume that diversity increases unbounded through time, as is typical in molecular phylogenetic studies. If clade diversity is regulated by ecological factors, then species richness may be independent of clade age and it may not be possible to infer the rate at which diversity arose. This has substantial consequences for the interpretation of many studies that have contrasted rates of diversification among clades and regions. Often, it is possible to estimate the total diversification experienced by a clade but not diversification rate itself. I show that the evidence for ecological limits on diversity in higher taxa is widespread. Finally, I explore the implications of ecological limits for a variety of ecological and evolutionary questions that involve inferences about speciation and extinction rates from phylogenetic data.     

Variations in the intertidal and subtidal macrofauna and sediments along a salinity gradient in the upper forth estuary

The intertidal and subtidal soft-sediment macrofauna of the upper Forth estuary, eastern Scotland, UK has been examined. The intertidal fauna was sampled in 1977, and again in 1988/89, at up to twelve stations along the salinity gradient. The subtidal fauna was sampled in 1982 and in 1988/89 at up to 15 stations. The stations span the region of the freshwater-seawater interface, and area of the turbidity maximum. Large spatial and temporal variations in macrofaunal abundance and species composition were observed. Sites at the head of the estuary with low salinity were dominated by oligochaetes, but more saline areas were characterised by a depauparate estuarine fauna. The area has historically received large quantities of organic waste both from sewage and industrial discharges which supported very high abundances of oligochaetes of up to 500,000 m⁻² in the upper reaches of the estuary. Reductions in the organic inflow to the area since the early-1980's have begun to cause reductions in oligochaete populations and also allowed the further penetration intertidally of non-oligochaete species into the upper and middle reaches of the estuary. No comparable upstream penetration by the non-oligochaete subtidal fauna has been observed, possibly on account of the greater sediment instability in the estuary's main channel.     

Searching factors causing implausible non-monophyly: ssu rDNA phylogeny of Isopoda Asellota (Crustacea: Peracarida) and faster evolution in marine than in freshwater habitats

This contribution addresses two questions: which alignment patterns are causing non-monophyly of the Asellota and what is the phylogenetic history of this group? The Asellota are small benthic crustaceans occurring in most aquatic habitats. In view of the complex morphological apomorphies known for this group, monophyly of the Asellota has never been questioned. Using ssu rDNA sequences of outgroups and of 16 asellote species from fresh water, littoral marine habitats and from deep-sea localities, the early divergence between the lineages in fresh water and in the ocean, and the monophyly of the deep-sea taxon Munnopsidae are confirmed. Relative substitution rates of freshwater species are much lower than in other isopod species, rates being highest in some littoral marine genera (Carpias and Jaera). Furthermore, more sequence sites are variable in marine than in freshwater species, the latter conserve outgroup character states. Monophyly is recovered with parsimony methods, but not with distance and maximum likelihood analyses, which tear apart the marine from the freshwater species. The information content of alignments was studied with spectra of supporting positions. The scarcity of signal (=apomorphic nucleotides) supporting monophyly of the Asellota is attributed to a short stem-line of this group or to erosion of signal in fast evolving marine species. Parametric boostrapping in combination with spectra indicates that a tree model cannot explain the data and that monophyly of the Asellota should not be rejected even though many topologies do not recover this taxon.     

Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae

Marine–freshwater and freshwater–marine transitions have been key events in the evolution of life, and most major groups of organisms have independently undergone such events at least once in their history. Here, we first compile an inventory of bidirectional freshwater and marine transitions in multicellular photosynthetic eukaryotes. While green and red algae have mastered multiple transitions in both directions, brown algae have colonized freshwater on a maximum of six known occasions, and angiosperms have made the transition to marine environments only two or three times. Next, we review the early evolutionary events leading to the colonization of current habitats. It is commonly assumed that the conquest of land proceeded in a sequence from marine to freshwater habitats. However, recent evidence suggests that early photosynthetic eukaryotes may have arisen in subaerial or freshwater environments and only later colonized marine environments as hypersaline oceans were diluted to the contemporary level. Although this hypothesis remains speculative, it is important to keep these alternative scenarios in mind when interpreting the current habitat distribution of plants and algae. Finally, we discuss the roles of structural and functional adaptations of the cell wall, reactive oxygen species scavengers, osmoregulation, and reproduction. These are central for acclimatization to freshwater or to marine environments. We observe that successful transitions appear to have occurred more frequently in morphologically simple forms and conclude that, in addition to physiological studies of euryhaline species, comparative studies of closely related species fully adapted to one or the other environment are necessary to better understand the adaptive processes.     

Changes in carbon and nitrogen content during decomposition of three macrophytes in freshwater and marine environments

Three species of aquatic plants were analyzed for their ash, organic carbon and nitrogen content both fresh and after decomposition using the mesh bag method Chara contraria A. Br. ex Kütz in a small freshwater pond and Lemna minor L. in a shallow swamp were examined over a 70 day period of in situ decomposition. Fucus vesiculosus L. was examined over a 63 day period of decomposition in a rocky shore and a salt marsh environment.During decomposition Chara showed a decrease in carbon and an increase in nitrogen content while Lemna increased in carbon and decreased in nitrogen, all on an ash-free dry weight basis. Although the C : N ratio of Chara was high initially and that of Lemna relatively low, after decomposition the C : N ratio for the remains of the two plants was nearly the same. Fucus decomposing in the salt marsh showed no significant change in carbon but increased in nitrogen content while that at the rocky shore decreased in carbon and increased in nitrogen content. Much of the loss in total dry weight in the first few hours of submergence could be attributed to solubilization of ash and of some high C : N ratio organic material. Consistent and significant differences in the C : N ratio of decomposing Fucus at the two marine sites may be attributable to the nature of the decomposer organisms that inhabit these environments. The accumulation of a high proportion of autotrophic microbial biomass (such as purple sulfur bacteria) in the structural carbohydrates of the salt marsh Fucus may have caused these differences.This study suggests that initial differences in nutritional value of aquatic macrophytes diminish during decomposition and that the ultimate C : N ratio attained may be more dependent on the nature of the decomposer organisms present than on the nature of the organic material undergoing decomposition.     

Trophic level asynchrony in rates of phenological change for marine,freshwater and terrestrial environments

Recent changes in the seasonal timing (phenology) of familiar biological events have been one of the most conspicuous signs of climate change. However, the lack of a standardized approach to analysing change has hampered assessment of consistency in such changes among different taxa and trophic levels and across freshwater, terrestrial and marine environments. We present a standardized assessment of 25 532 rates of phenological change for 726 UK terrestrial, freshwater and marine taxa. The majority of spring and summer events have advanced, and more rapidly than previously documented. Such consistency is indicative of shared large scale drivers. Furthermore, average rates of change have accelerated in a way that is consistent with observed warming trends. Less coherent patterns in some groups of organisms point to the agency of more local scale processes and multiple drivers. For the first time we show a broad scale signal of differential phenological change among trophic levels; across environments advances in timing were slowest for secondary consumers, thus heightening the potential risk of temporal mismatch in key trophic interactions. If current patterns and rates of phenological change are indicative of future trends, future climate warming may exacerbate trophic mismatching, further disrupting the functioning, persistence and resilience of many ecosystems and having a major impact on ecosystem services.     

Temporal and spatial trends in heavy metal concentrations in the marine mussel Mytilus edulis from the Western Scheldt estuary (The Netherlands)

Since the first North Sea Conference (1984, Bremen), all countries bordering the North Sea made commitments to reduce discharge of hazardous substances into the North Sea. From Belgium and The Netherlands, large reductions (upto 90) in heavy metal emissions from land-based sources have been reported between 1985 and 2000. Recently, some studies in the Western Scheldt estuary (WS) have shown that total metal concentration in the water, sediments and suspended particles have decreased compared to levels in the 70s. However, data on aquatic organisms is still very limited and it is therefore difficult to confirm whether the reductions in pollution input and generally improving water quality in the WS have a corresponding impact on the levels of heavy metals in aquatic organisms. The current study measured metal concentrations in the soft tissues of mussels, Mytilus edulis (known to be good indicators of environmental metal pollution) during the period 1996–2002. Spatial (salinity and pollution gradients), temporal and seasonal variations were also studied. Results showed a down-stream decreasing trend for the metals studied (Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb and Zn) during all sampling campaigns. There was also a significant seasonal effect on tissue metal concentrations, with a peak observed around spring in both WS and the nearby less polluted Eastern Scheldt (ES). On temporal trends, a clear drop of metals in mussels was observed in the early 80s coinciding with the start of the efforts to reduce chemical pollution input into the North Sea. Since those early reductions, metal concentrations in mussels generally remained unchanged upto mid 90s. However, in recent times metal concentration in mussels have increased significantly, for example Cd in 2002 was almost 10 times the values in 1983 and similar to levels seen during the peak in the 70s. Other metals also increased in the 90s also reaching levels seen in the 70s. As there is no indication of recent increase in metal input into the estuary, we suggest that increased metal concentrations observed in mussels in recent years especially in the upper estuary are most likely a result of changes in physical and chemical speciation and metal bioavailability. Such changes may be caused by changes in some water quality parameters in the estuary (i.e. increased dissolved oxygen, concentration of organic matter), resulting in conditions that favour releases of sediment-bound metals into the water column. The relationship between metal content and season showed very similar annual profiles in the polluted WS and less polluted ES. Thus, seasonal variations in metal concentrations appear to be largely controlled by biological processes, while total body burdens are dependent on environmental levels and bioavailability.     

Cladogenesis and loss of the marine life-history phase in freshwater galaxiid fishes (Osmeriformes: Galaxiidae)

Switches from migratory (diadromous) to nonmigratory (freshwater) life histories are known to have occurred repeatedly in some aquatic taxa. However, the significance of the loss of diadromy as an initiator for speciation remains poorly understood. The rivers of New Zealand's South Island house a species flock of recently derived nonmigratory galaxiid fishes known as the Galaxias vulgaris complex. Members of this complex are morphologically and genetically similar to the diadromous G. brevipinnis found in New Zealand and southeastern Australia. We hypothesised that South Island's G. vulgaris complex (at least 10 nonmigratory lineages) represents a number of independent radiations from a migratory G. brevipinnis stock, with repeated loss of diadromy. Sequence data were obtained for 31 ingroup samples (G. vulgaris complex and G. brevipinnis) plus four outgroup taxa. A well-resolved phylogeny based on 5039 base pairs of the mitochondrial genome suggests that diadromy has been lost on three separate occasions. Thus, speciation in these galaxiid fishes is partly an incidental phenomenon caused by switches from diadromous to nonmigratory strategies. However, much of the subsequent nonmigratory diversity is monophyletic, suggesting that drainage evolution (vicariance) has also played a major role in cladogenesis. Levels of sequence divergence among major ingroup lineages (1.6-12.7%) suggest that the radiation is considerably older relative to Northern Hemisphere (postglacial) complexes of salmonid, osmerid, and gasterosteid fishes. Sympatric taxa are not monophyletic, suggesting that their coexistence reflects secondary contact rather than sympatric speciation. The monophyly of New Zealand G. brevipinnis is well supported, but both mitochondrial DNA and nuclear sequences indicate that G. brevipinnis is paraphyletic on an intercontinental scale. The divergence (maximum 11.5%) between Tasmanian and New Zealand G. brevipinnis, although large, supports marine dispersal rather than vicariance as the principle biogeographic mechanism on an intercontinental scale.     

Disintegrating over space and time: Paraphyly and species delimitation in the Wehrle's Salamander complex

Accurate species delimitation is critical for biodiversity studies. However, species complexes characterized by introgression, high levels of population structure and subtle phenotypic differentiation can be challenging to delimit. Here, we report on a molecular systematic investigation of the woodland salamanders Plethodon wehrlei and Plethodon punctatus, which traditionally have been placed in the Plethodon wehrlei species group. To quantify patterns of genetic variation, we collected genetic samples from throughout the range of both species, including 22 individuals from nine populations of P. punctatus, and 60 individuals from 26 populations of P. wehrlei. From these samples, we sequenced three mtDNA loci (5596 base pairs) and five nuclear loci (3377 base pairs). We inferred time‐calibrated gene trees and species trees using BEAST 2.4.6, and we delimited putative species using a Bayesian implementation of the general mixed Yule‐coalescent model (bGMYC) and STRUCTURE. Finally, we validated putative species using the multispecies coalescent as implemented in Bayesian Phylogenetics and Phylogeography (BPP). We found substantial phylogeographic diversity in P. wehrlei, including multiple geographically cohesive clades and an inferred mitochondrial common ancestor at 11.5 myr (95% HPD: 9.6–13.6 myr) that separated populations formerly assigned to P. dixi from all other populations. We also found that P. punctatus is deeply nested within P. wehrlei, rendering the latter paraphyletic. After discussing the challenges faced by modern species delimitation methods, we recommend retaining P. punctatus because it is ecologically and phenotypically distinct. We further recommend that P. dixi be recognized as a valid species.     

Mate recognition in a freshwater fish: geographical distance, genetic differentiation, and variation in female preference for local over foreign males

It often is assumed that more distant allopatry should reflect reduced rates of contemporary gene flow and/or greater divergence in mate recognition systems. This assumption, however, is rarely tested and may not always be appropriate. Here we investigated female preference for local and foreign males in a morphologically variable Australian freshwater fish, the Pacific blue-eye Pseudomugil signifer. Using a multidisciplinary approach that combined molecular phylogeography with conventional mate choice experiments, we found female blue-eyes spent more time in association with local males only when the alternative was a foreigner from a geographically and genetically more distant population. When offered the choice between two foreign males, females associated more with males from the population that was more closely adjacent to their own. Our results suggest that female preference for local over foreign males in blue-eyes may depend on how genetically and geographically separated populations are from one another.     

Identification of novel microRNA genes in freshwater and marine ecotypes of the three‐spined stickleback (Gasterosteus aculeatus)

The three‐spined stickleback (Gasterosteus aculeatus L.) is an important model organism for studying the molecular mechanisms of speciation and adaptation to salinity. Despite increased interest to microRNA discovery and recent publication on microRNA prediction in the three‐spined stickleback using bioinformatics approaches, there is still a lack of experimental support for these data. In this paper, high‐throughput sequencing technology was applied to identify microRNA genes in gills of the three‐spined stickleback. In total, 595 miRNA genes were discovered; half of them were predicted in previous computational studies and were confirmed here as microRNAs expressed in gill tissue. Moreover, 298 novel microRNA genes were identified. The presence of miRNA genes in selected ‘divergence islands’ was analysed and 10 miRNA genes were identified as not randomly located in ‘divergence islands’. Regulatory regions of miRNA genes were found enriched with selective SNPs that may play a role in freshwater adaptation.